In response to your feedback, we’ve made more whole genome cross-species alignments available in NCBI’s Comparative Genome Viewer (CGV). You can use these alignments to explore genome rearrangements between species. You can also zoom in to analyze regions of conserved gene synteny.
There are over 20 new cross-species alignments available, including human-mouse, mouse-rat, human-chimp, human-cattle, dog-cat, and others! These cross-species alignments provide additional opportunities to explore evolutionary relationships at the genomic and gene levels. We will add more cross-species alignments in the coming months.
The latest cross-species alignments added to CGV include imports from the UCSC Genomics Institute, as well as those generated at NCBI.
Check out two examples of cross-species whole-genome alignments in CGV below (Figure 1).
Figure 1. Whole genome alignments between (A) mouse and human (GRCm39 vs. GRCh38.p14) and (B) cat and dog (F.catus_Fca126_mat1.0 vs. ROS_Cfam_1.0). Colored bands connects aligned regions; green indicates same orientation, blue indicates opposite orientation.
When you zoom in on an alignment (Figure 2), you can compare gene annotation on the two assemblies and see the extent of conservation of synteny. You can also see which genes are missing from one or the other assembly, indicating changes in sequence or differences in annotation.
We are excited to announce an update to NCBI’s Comparative Genome Viewer (CGV) that allows you to quickly determine the relative orientation of aligned segments.CGV displays whole genome alignments between two different eukaryotic assemblies (Figure 1).
In the viewer, individual alignment regions are connected by colored bands between two chromosomes. These alignments are now colored differently depending on whether the aligned sequences on the two assemblies are in the same orientation (forward) or reverse orientation relative to one another. Forward orientation alignments are connected by green bands, whereas reverse alignments are connected by purple bands. Reverse alignments represent local genome inversions or inverted translocations and may point to areas of significant biological difference between the two assemblies. Continue reading “New feature in the Comparative Genome Viewer!”→
The potential impact of emerging model organisms on human health
Comparative genomics is a science that compares genomic data either within a species or across species to answer questions in biomedicine. Laboratory experiments can then investigate the functional impact of those genomics similarities and differences. The history of comparative genomics goes back to the mid-1990s, but comparative genomics is now accelerating. A flood of new data is emerging as DNA sequencing technology becomes cheaper and commoditized. While this growth poses many challenges to current tools and approaches, it also offers immense opportunity for scientific research and understanding. These insights continue to reveal novel model organisms that can further the impact of comparative genomics on human health. Continue reading “NIH Comparative Genomics Resource project”→
New search feature in the Comparative Genome Viewer (CGV)
You asked, we listened! We are pleased to announce that you can now search for a gene in NCBI’s Comparative Genome Viewer (CGV) and navigate directly to its location in the viewer.
Maybe you’re studying a particular gene or gene family, and you want to see if that gene is annotated in the assemblies you’re viewing. Or maybe you know that a gene is annotated on one of the assemblies, but you want to obtain the coordinates of the aligned region on an unannotated assembly. These coordinates may help you find the ortholog for the gene in the aligned assembly.
Learn about the NIH Comparative Genomics Resource (CGR) Project
The Biodiversity Genomics conference will take place virtually, October 2-7, 2022. This event is hosted by the Earth BioGenome Project and is open and free for all to attend.
NCBI staff will present a variety of recorded talks and posters highlighting various elements of the NIH Comparative Genomics Resource (CGR), including NCBI Datasets and the Comparative Genome Viewer (CGV). CGR is a multi-year National Library of Medicine (NLM) project to maximize the impact of eukaryotic research organisms and their genomic data resources to biomedical research. NCBI is charged with leading CGR development and engaging genomics communities. The CGR project will facilitate reliable comparative genomics analyses for all eukaryotic organisms in collaboration with the genomics community.
NLM’s NCBI is introducing the Comparative Genome Viewer (CGV), an easy-to-use visualization tool that helps you quickly compare eukaryotic genome assemblies and easily identify genomic changes that may be significant to biology and evolution. With the new CGV you can view and compare the alignment between two assemblies to see differences in genomic sequence and structure, including deletions, inversions, and translocations. Currently, you can compare assemblies from over 50 annotated animal and plant genomes.